The Filipinos led Thailand and Korea by a stroke heading to the par-5 final hole. But Pagunsan hit his drive into the water and again on his second shot for a costly seven that ruined the RP campaign.
Thailand went on to sweep both the team and individual awards, beating Korea by one and the Filipinos by three with a 563 total.
Prom Meesawat took the individual title in runaway fashion, winning over Pagunsan and Hye Dong Kim by nine shots with four consecutive rounds in the 60s, including a final-day 67 for 268.
Pagunsan had a last-day 72 while Marlon Dizon scored 71 to place 10th in the individual category.
Malaysia wound up fourth, Taiwan fifth, Thailand B sixth, India seventh, Thailand-South eighth, Thailand-North ninth and Thailand North-East 10th.